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RNA relics and origin of life.

Demongeot J, Glade N, Moreira A, Vial L - Int J Mol Sci (2009)

Bottom Line: A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin.On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity.We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions.

View Article: PubMed Central - PubMed

Affiliation: University Joseph Fourier of Grenoble, TIMC-IMAG UMR UJF/CNRS, La Tronche, France. Jacques.Demongeot@imag.fr <Jacques.Demongeot@imag.fr>

ABSTRACT
A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.

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Related in: MedlinePlus

Schematic view of regulatory processes that can occur in a cell. Positive and negative classical regulations as well as syntheses are shown as black arrows. Negative regulations due to miRs and siRNAs are indicated as red arrows. A possible contextual down-regulation (dashed red lines) could come from direct interaction between metabolites (amino-acids and their derivatives, or energetic nucleotides) and RNA or DNA sequences.
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f9-ijms-10-03420: Schematic view of regulatory processes that can occur in a cell. Positive and negative classical regulations as well as syntheses are shown as black arrows. Negative regulations due to miRs and siRNAs are indicated as red arrows. A possible contextual down-regulation (dashed red lines) could come from direct interaction between metabolites (amino-acids and their derivatives, or energetic nucleotides) and RNA or DNA sequences.

Mentions: Usually, the feedback action of the metabolism on the activity of the genes is only understood to be mediated by “sensors” (protein receptors) of particular metabolites. Those sensing molecules transmit the metabolic state of the cell to the genes and up or down regulate them. Another source of “global” regulation is the RNA interference (siRNAs) combined to the miRs and RNA-binding oligo-peptides activity [28]. It is due to the random garbage production of small sequences of RNA from the destruction of functional RNAs (mRNAs, tRNAs ...). Usually it is not really considered as a regulatory process and then called interference, but one can consider that even if these products are random, they apply a global down regulation to the cell machinery, so the living organisms had to develop (during evolution) robust and very efficient systems to survive despite of the presence of RNA interference. This natural process acts as a filter of efficiency of cell machinery subsystems. Direct interactions between metabolites (notably amino-acids) and RNA or DNA could be also viewed as interference, but we suggest that it shall be viewed as a context-dependent regulatory process. The internal levels of metabolites of an organism will depend on what it “eats”. When cells are cultured in media rich in certain metabolites, they adapt their metabolic pathways to use such metabolites, but in the same time, according to the stereo-chemical direct interactions, the same metabolites will exert a negative feedback on some cell functions because they will act as competitors with the tRNAs. What is amazing is that this regulatory process is specific since the targets concerned are the codons that stereo-chemically fit with the amino-acids: for example, if the medium becomes rich in Tyrosine and independently of its internal cell concentration, a negative feedback will appear that will inhibit the formation of all proteins that contain Tyrosine residues. Of course, such an inhibition should be very weak, but it could act as a bias on cell activity. At a rougher level, the same can be said with single nucleotides such as energetic nucleotides (ATP, GTP), that could slow down the formation of proteins whose mRNAs are rich in complementarity bases (resp. Uracil and Cytosine). Such a situation could occur when cells are in particular energy states. In Figure 9, a schematic view of cell regulation is proposed, showing in dashed red lines the negative feedback the metabolism could exert on the cell machinery and on the genome.


RNA relics and origin of life.

Demongeot J, Glade N, Moreira A, Vial L - Int J Mol Sci (2009)

Schematic view of regulatory processes that can occur in a cell. Positive and negative classical regulations as well as syntheses are shown as black arrows. Negative regulations due to miRs and siRNAs are indicated as red arrows. A possible contextual down-regulation (dashed red lines) could come from direct interaction between metabolites (amino-acids and their derivatives, or energetic nucleotides) and RNA or DNA sequences.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2812825&req=5

f9-ijms-10-03420: Schematic view of regulatory processes that can occur in a cell. Positive and negative classical regulations as well as syntheses are shown as black arrows. Negative regulations due to miRs and siRNAs are indicated as red arrows. A possible contextual down-regulation (dashed red lines) could come from direct interaction between metabolites (amino-acids and their derivatives, or energetic nucleotides) and RNA or DNA sequences.
Mentions: Usually, the feedback action of the metabolism on the activity of the genes is only understood to be mediated by “sensors” (protein receptors) of particular metabolites. Those sensing molecules transmit the metabolic state of the cell to the genes and up or down regulate them. Another source of “global” regulation is the RNA interference (siRNAs) combined to the miRs and RNA-binding oligo-peptides activity [28]. It is due to the random garbage production of small sequences of RNA from the destruction of functional RNAs (mRNAs, tRNAs ...). Usually it is not really considered as a regulatory process and then called interference, but one can consider that even if these products are random, they apply a global down regulation to the cell machinery, so the living organisms had to develop (during evolution) robust and very efficient systems to survive despite of the presence of RNA interference. This natural process acts as a filter of efficiency of cell machinery subsystems. Direct interactions between metabolites (notably amino-acids) and RNA or DNA could be also viewed as interference, but we suggest that it shall be viewed as a context-dependent regulatory process. The internal levels of metabolites of an organism will depend on what it “eats”. When cells are cultured in media rich in certain metabolites, they adapt their metabolic pathways to use such metabolites, but in the same time, according to the stereo-chemical direct interactions, the same metabolites will exert a negative feedback on some cell functions because they will act as competitors with the tRNAs. What is amazing is that this regulatory process is specific since the targets concerned are the codons that stereo-chemically fit with the amino-acids: for example, if the medium becomes rich in Tyrosine and independently of its internal cell concentration, a negative feedback will appear that will inhibit the formation of all proteins that contain Tyrosine residues. Of course, such an inhibition should be very weak, but it could act as a bias on cell activity. At a rougher level, the same can be said with single nucleotides such as energetic nucleotides (ATP, GTP), that could slow down the formation of proteins whose mRNAs are rich in complementarity bases (resp. Uracil and Cytosine). Such a situation could occur when cells are in particular energy states. In Figure 9, a schematic view of cell regulation is proposed, showing in dashed red lines the negative feedback the metabolism could exert on the cell machinery and on the genome.

Bottom Line: A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin.On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity.We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions.

View Article: PubMed Central - PubMed

Affiliation: University Joseph Fourier of Grenoble, TIMC-IMAG UMR UJF/CNRS, La Tronche, France. Jacques.Demongeot@imag.fr <Jacques.Demongeot@imag.fr>

ABSTRACT
A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.

Show MeSH
Related in: MedlinePlus